I've finallly got the ducks in order, The command mpirun -np 8 gmx_mpi mdrun -deffnm PVP20k.nvt auto maps the process as: On host xxx 2 GPUs auto-selected for this run. Mapping of GPU IDs to the 8 GPU tasks in the 8 ranks on this node: PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1
this for the 32 core 2990 AMD TR. DLB is taking some time and I will be tuning the system today. but it works. Results for 80k atoms will be reported. Thank you all. Paul Sent from Mailspring (https://getmailspring.com/), the best free email app for work On Dec 19 2018, at 11:36 am, p buscemi <pbusc...@q.com> wrote: > Getting closer... > ( thinking a bit about the initial command structure does help....) > > Now using the command: > gmx_mpi mdrun -deffnm PVP20k.nvt -nb gpu -ntomp 16 -npme 4 > :-) GROMACS - gmx mdrun, 2018.4 (-: > > gets past the v5 issue but a new nastygram is sent... > "The -dd or -npme option request a parallel simulation, but gmx mdrun was not > started through mpirun/mpiexec or only one rank was requested through > mpirun/mpiexec" > > Inclusion of mpirun was attempted but I've not hit the proper format. > Paul > > > > > Sent from Mailspring (https://getmailspring.com/), the best free email app > for work > On Dec 19 2018, at 11:08 am, pbusc...@q.com wrote: > > Thank you - both - very much again. > > > > The "mpir_run -npx gmx -mdrun....." command was lifted from a Feb 2018 > > response from Szilard , to a multi gpu, user which he used as an example. > > > > I'll crank on your pointers right now. > > Paul > > -----Original Message----- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Justin > > Lemkul > > Sent: Wednesday, December 19, 2018 10:47 AM > > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > > Subject: Re: [gmx-users] error on opening gmx_mpi > > > > On Wed, Dec 19, 2018 at 11:44 AM p buscemi <pbusc...@q.com> wrote: > > > Shi, > > > reinstalling the mpi version using gmx 18.4 did not help........any > > ideas ? > > > hms@rgb2 ~/Desktop/PVP20k $ mpirun -np 8 mdrun_mpi -deffnm PVP20k1.em > > > :-) GROMACS - mdrun_mpi, VERSION 5.1.2 (-: > > > > > > > > You're just calling the same (incorrect) command again. You installed > > "gmx_mpi" version 2018.4 but then your command uses "mdrun_mpi" instead. > > Apparently you have version 5.1.2 (perhaps from a package manager, based > > on the fact that it's installed in /usr/bin instead of > > /usr/local/gromacs/bin) that is being found in your PATH. > > > > If you've got multiple versions installed, either source GMXRC properly or > > use full PATH information in your commands. Above all, use the right > > binary name to start :) > > > > -Justin > > -- > > ========================================== > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > > > ========================================== > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > > a mail to gmx-users-requ...@gromacs.org. > > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.